Dear Phil, 0.32 is awfully close to 1/3, which brings a nice mathematical puzzle to my mind to see if the 1/3 occupancy is somehow related to the 3 fully occupied monomers... It may also be related to a (trigonal??) space group...
You probably have already tried it, but phaser has the option to give it already solved molecules and ask it to search for additional molecules. Here I would indeed lower the expected % homology significantly, to crudely compensate for the low occupancy. In contrast to the advice of Dale, I would play around with the % homology to find the value which works best. My 2 cents, Herman -----Ursprüngliche Nachricht----- Von: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> Im Auftrag von Phil Jeffrey Gesendet: Donnerstag, 10. Dezember 2020 14:49 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Finding partial occupancy monomer by MR ? Preamble: I have an interesting crystal form with 3 monomers (~400aa) at full occupancy and apparently one at much reduced occupancy. It was built recently from Se-SAD and was in moderately good condition: Rfree=32% for trimer, 2.6 Å. In recent refinement cycles it became obvious that there was a 4th monomer in a region of weaker/choppy 2Fo-Fc and Fo-Fc density that corresponded to a "confusing" set of low-occupancy SeMet sites found by SHELXD and Phaser-EP. The experimental map was bad in that region and was probably flattened during density modification anyway, in retrospect. Question: Phaser failed to find the 4th monomer after trivially finding the other 3 with a recent version of the monomer. I'm wondering if there's a way to indicate "this one is partial occupancy" to Phaser, or if there's a way to improve the odds of success beyond just lowering the expected % homology. Or if anyone has had success with other programs. This is perhaps a rare edge case but I naively expected Phaser to work. In the end I used the weak SeMet sites to locate the monomer and the occupancy appears to be around 0.32 in refinement. Cheers, Phil Jeffrey Princeton ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=04%7C01%7CHerman.Schreuder%40SANOFI.COM%7C5ee2ee2e87f04d853f0408d89d126615%7Caca3c8d6aa714e1aa10e03572fc58c0b%7C0%7C1%7C637432050077999989%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=G28AUNQrAgQYblmaYBVnXESTXiekmWzfTLPMMX%2B%2BOgw%3D&reserved=0 This message was issued to members of https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2FCCP4BB&data=04%7C01%7CHerman.Schreuder%40SANOFI.COM%7C5ee2ee2e87f04d853f0408d89d126615%7Caca3c8d6aa714e1aa10e03572fc58c0b%7C0%7C1%7C637432050077999989%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=WitzjV%2F3hzx1SzMmmDzKVX56uVBD1fXluDDAcyY8Y1g%3D&reserved=0, a mailing list hosted by https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2F&data=04%7C01%7CHerman.Schreuder%40SANOFI.COM%7C5ee2ee2e87f04d853f0408d89d126615%7Caca3c8d6aa714e1aa10e03572fc58c0b%7C0%7C1%7C637432050077999989%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=wv3OjpY8AGsTj0RfiiEMjWPLDD5QOMvfV1TwcaRXczs%3D&reserved=0, terms & conditions are available at https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fpolicyandsecurity%2F&data=04%7C01%7CHerman.Schreuder%40SANOFI.COM%7C5ee2ee2e87f04d853f0408d89d126615%7Caca3c8d6aa714e1aa10e03572fc58c0b%7C0%7C1%7C637432050077999989%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=mEy2Z2rqn8IBmLklgmDe0%2BZOXq4gcLHqSqze6fW%2Fhx4%3D&reserved=0 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
